So I did some research and it seems like the 3.5 Ecoboost motor uses an eBOV (electronic blow off valve, although technically it really should be called an electronic re-circulation valve as it release the boost back into the intake system). The eBOV is attached directly to the intercooler. This video is from a 1st gen 3.5 ecoboost, but you can see it here: https://youtu.be/V-bdHOzVHUc?t=83
There is an intake manifold pressure sensor attached to the top of the top of the manifold that tells the ECU when to open the eBOV. Same video, can be seen here:
https://youtu.be/V-bdHOzVHUc?t=216
After some more searching, it seems like people have had issues with the eBOV staying open for longer than it should, usually due to a torn internal diaphragm. The issue is fixed by replacing the eBOV. See this thread: BOV staying open under load... 2013 FX4 SCREW - Page 3
You can try convincing your dealer you know what the issue is, but that generally doesn't go over too well. You can also try replacing the part yourself, but that is $ out of your pocket and you run the risk that it is actually something else all together.
Let us know how it goes.
When this happens should there be an engine parameter that's out of wack that you can see with a data logger? I assume it doesn't set a code, so I might have answered my own question.
Mike